Atomistry » Cadmium » PDB 3zr9-4efp » 4bpk
Atomistry »
  Cadmium »
    PDB 3zr9-4efp »
      4bpk »

Cadmium in PDB 4bpk: Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5

Protein crystallography data

The structure of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5, PDB code: 4bpk was solved by B.J.Smith, E.F.Lee, J.W.Checco, S.H.Gellman, W.D.Fairlie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 36.066 / 1.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 65.175, 72.133, 80.579, 90.00, 90.00, 90.00
R / Rfree (%) 21.92 / 25.22

Cadmium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Cadmium atom in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 (pdb code 4bpk). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 19 binding sites of Cadmium where determined in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5, PDB code: 4bpk:
Jump to Cadmium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Cadmium binding site 1 out of 19 in 4bpk

Go back to Cadmium Binding Sites List in 4bpk
Cadmium binding site 1 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 1 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1196

b:44.4
occ:0.68
CD A:CD1196 0.0 44.4 0.7
CD A:CD1196 2.0 45.3 0.3
OE2 A:GLU129 2.4 44.7 1.0
O A:HOH2059 2.5 47.2 1.0
CD A:GLU129 3.4 43.6 1.0
OE1 A:GLU129 3.9 40.3 1.0
CB C:ALA7 3.9 43.7 1.0
NH2 C:ARG10 4.0 43.7 1.0
CG A:GLU129 4.7 36.8 1.0

Cadmium binding site 2 out of 19 in 4bpk

Go back to Cadmium Binding Sites List in 4bpk
Cadmium binding site 2 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 2 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1196

b:45.3
occ:0.32
CD A:CD1196 0.0 45.3 0.3
CD A:CD1196 2.0 44.4 0.7
OE2 A:GLU129 2.4 44.7 1.0
OE1 A:GLU129 2.5 40.3 1.0
CD A:GLU129 2.8 43.6 1.0
O A:HOH2059 3.7 47.2 1.0
CD A:ARG132 3.8 57.7 0.5
NH2 C:ARG10 4.3 43.7 1.0
CG A:GLU129 4.3 36.8 1.0
NE A:ARG132 4.3 60.0 0.5
NE A:ARG132 4.4 60.7 0.5
CG A:ARG132 4.6 59.2 0.5
CG A:ARG132 4.8 57.7 0.5
NH2 A:ARG132 4.8 49.9 0.5
CZ A:ARG132 4.9 56.1 0.5
CD A:ARG132 5.0 61.2 0.5

Cadmium binding site 3 out of 19 in 4bpk

Go back to Cadmium Binding Sites List in 4bpk
Cadmium binding site 3 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 3 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1197

b:56.4
occ:1.00
O A:HOH2042 2.3 53.8 1.0
OE2 A:GLU92 2.4 44.0 1.0
O A:HOH2043 2.4 55.2 1.0
O A:HOH2023 2.5 43.1 1.0
CD A:GLU92 3.3 46.9 1.0
OE1 A:GLU92 3.6 49.9 1.0
O A:SER18 3.8 40.1 0.7
O A:SER18 3.9 42.8 0.3
NE2 A:GLN88 4.2 36.8 1.0
O A:HOH2008 4.3 61.8 1.0
CG A:GLN88 4.3 35.7 1.0
O A:HOH2035 4.4 38.6 0.4
CG A:GLU92 4.6 41.4 1.0
CD A:GLN88 4.7 38.1 1.0
C A:SER18 4.8 40.2 0.3
C A:SER18 4.8 40.4 0.7
CB A:SER18 5.0 37.0 0.7

Cadmium binding site 4 out of 19 in 4bpk

Go back to Cadmium Binding Sites List in 4bpk
Cadmium binding site 4 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 4 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1198

b:69.0
occ:1.00
CD2 A:HIS113 2.8 56.7 0.5
NE2 A:HIS113 2.9 56.2 0.5
ND1 A:HIS113 3.2 62.3 0.5
CE1 A:HIS113 3.7 63.0 0.5
CG A:HIS113 4.0 57.9 0.5
CE1 A:HIS113 4.1 56.2 0.5
CG A:HIS113 4.3 62.6 0.5
O A:HOH2066 4.4 57.4 1.0
NZ A:LYS157 4.6 64.7 1.0
ND1 A:HIS113 4.7 52.2 0.5
CB A:HIS113 4.8 60.0 0.5
NE2 A:HIS113 4.9 64.4 0.5

Cadmium binding site 5 out of 19 in 4bpk

Go back to Cadmium Binding Sites List in 4bpk
Cadmium binding site 5 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 5 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1199

b:46.9
occ:1.00
OE1 A:GLU153 2.3 49.7 1.0
O A:HOH2051 2.4 56.5 1.0
O A:HOH2065 2.4 46.1 1.0
O A:HOH2064 2.4 70.3 1.0
OE2 A:GLU153 2.4 51.0 1.0
O A:HOH2066 2.6 57.4 1.0
CD A:GLU153 2.7 41.0 1.0
CE A:LYS157 4.0 55.6 1.0
CG A:GLU153 4.2 38.0 1.0
O A:HOH2050 4.3 59.3 1.0
O A:LEU112 4.5 58.3 1.0
O A:HOH2063 4.6 42.4 1.0
NZ A:LYS157 4.6 64.7 1.0
OD2 A:ASP156 4.8 52.0 1.0
O A:THR109 4.9 44.1 1.0
CB A:GLU153 5.0 35.0 1.0
O A:SER110 5.0 51.7 1.0

Cadmium binding site 6 out of 19 in 4bpk

Go back to Cadmium Binding Sites List in 4bpk
Cadmium binding site 6 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 6 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1200

b:62.3
occ:0.45
CD A:CD1200 0.0 62.3 0.5
CD A:CD1200 1.8 64.1 0.6
CE1 A:HIS177 2.6 56.9 0.6
NE2 A:HIS177 3.3 56.3 0.6
CE1 A:HIS177 3.3 56.5 0.4
ND1 A:HIS177 3.7 60.5 0.6
ND1 A:HIS177 4.0 57.4 0.4
NE2 A:HIS177 4.1 55.9 0.4
OD2 A:ASP176 4.3 69.2 0.4
CD2 A:HIS177 4.5 56.0 0.6
CB A:ASP176 4.5 63.8 0.4
CB A:ASP176 4.7 65.2 0.6
CG A:HIS177 4.7 56.5 0.6
OD2 A:ASP176 4.8 70.8 0.6
CG A:ASP176 4.9 67.9 0.4

Cadmium binding site 7 out of 19 in 4bpk

Go back to Cadmium Binding Sites List in 4bpk
Cadmium binding site 7 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 7 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1200

b:64.1
occ:0.55
CD A:CD1200 0.0 64.1 0.6
CD A:CD1200 1.8 62.3 0.5
CE1 A:HIS177 2.9 56.9 0.6
NE2 A:HIS177 3.1 56.3 0.6
CE1 A:HIS177 3.2 56.5 0.4
NE2 A:HIS177 3.5 55.9 0.4
ND1 A:HIS177 3.8 60.5 0.6
ND1 A:HIS177 4.0 57.4 0.4
CD2 A:HIS177 4.1 56.0 0.6
CD2 A:HIS177 4.4 53.9 0.4
CG A:HIS177 4.5 56.5 0.6
CG A:HIS177 4.7 53.4 0.4

Cadmium binding site 8 out of 19 in 4bpk

Go back to Cadmium Binding Sites List in 4bpk
Cadmium binding site 8 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 8 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd1201

b:53.8
occ:1.00
O A:HOH2069 2.2 51.0 1.0
O A:HOH2068 2.2 52.7 1.0
OE2 A:GLU179 2.4 61.9 1.0
OE1 A:GLU179 2.7 55.5 1.0
CD A:GLU179 2.9 58.5 1.0
N B:SER2 4.1 68.3 1.0
CG A:GLU179 4.4 54.4 1.0
ND2 B:ASN5 4.6 54.6 1.0
OD1 A:ASN175 4.6 60.7 1.0
CB B:SER2 4.7 84.5 1.0
CA B:SER2 5.0 76.0 1.0

Cadmium binding site 9 out of 19 in 4bpk

Go back to Cadmium Binding Sites List in 4bpk
Cadmium binding site 9 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 9 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1196

b:47.5
occ:1.00
OD1 B:ASP189 2.4 67.1 1.0
OD2 B:ASP189 2.4 57.7 1.0
O B:GLY186 2.6 40.8 1.0
CG B:ASP189 2.7 57.8 1.0
O B:HOH2069 2.7 58.9 1.0
C B:GLY186 3.3 40.9 1.0
CA B:GLY186 4.0 44.0 1.0
N B:GLY187 4.1 37.4 1.0
OG1 B:THR190 4.2 50.0 1.0
CB B:ASP189 4.2 53.0 1.0
CA B:GLY187 4.2 32.7 1.0
N B:THR190 4.8 38.5 1.0
C B:GLY187 4.8 36.7 1.0

Cadmium binding site 10 out of 19 in 4bpk

Go back to Cadmium Binding Sites List in 4bpk
Cadmium binding site 10 out of 19 in the Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd binding site number 10 of Bcl-Xl Bound to Alpha Beta Puma BH3 Peptide 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cd1197

b:47.7
occ:1.00
O B:HOH2073 2.3 77.7 1.0
O B:HOH2058 2.3 66.2 1.0
O B:HOH2074 2.4 56.2 1.0
OD2 B:ASP176 2.5 46.0 1.0
OD1 B:ASP176 2.6 46.1 1.0
CG B:ASP176 2.9 43.7 1.0
O B:HOH2061 4.0 59.2 1.0
CG2 B:THR172 4.0 30.1 1.0
CB B:ASP176 4.5 37.4 1.0
O B:HOH2060 4.9 34.8 1.0
O B:THR172 5.0 26.4 1.0

Reference:

B.J.Smith, E.F.Lee, J.W.Checco, M.Evangelista, S.H.Gellman, W.D.Fairlie. Structure-Guided Rational Design of Alpha/Beta-Peptide Foldamers with High Affinity For Bcl-2 Family Prosurvival Proteins. Chembiochem V. 14 1564 2013.
ISSN: ISSN 1439-4227
PubMed: 23929624
DOI: 10.1002/CBIC.201300351
Page generated: Fri Jul 19 17:00:53 2024

Last articles

Zn in 7Z70
Zn in 7Z6Z
Zn in 7Z6S
Zn in 7Z68
Zn in 7Z5U
Zn in 7YUJ
Zn in 7Z5A
Zn in 7Z1N
Zn in 7Z16
Zn in 7Z18
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy